Class: Organism Sample (OrganismSample)

name: OrganismSample
description: A material sample in which all cells are expected to share the same genome.
  This includes microbial colony picks, pellets from presumably pure liquid cultures,
  plant tissue clips, fungal fruiting body sections, and similar materials where the
  submitter intends to study a single organism. The purity expectation may be contradicted
  by sequencing results.
title: Organism Sample
comments:
- An OrganismSample is not necessarily pure. The submitter expects it to contain a
  single organism, but sequencing may reveal contamination. Purity and strain-verification
  fields (single-colony isolation, ribosomal sequences, fungal screening) are JGI
  submission logistics and live in submission-schema JgiIsolateInterface, not here.
- The expected_organism slot links to an Organism instance representing what the submitter
  believes is in the sample.
- The defining criterion is genomic homogeneity of intent, not material type. A bacterial
  colony pick, a plant leaf clip, and a fungal fruiting body section are all OrganismSamples
  because the submitter expects one genome. An algal mat, a cat fecal sample for microbiome
  study, or a soil sample are Biosamples because they contain communities of organisms.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://github.com/microbiomedata/nmdc-schema/issues/2803
- https://github.com/microbiomedata/nmdc-schema/issues/2961
close_mappings:
- OBI:0100051
is_a: Sample
slots:
- associated_studies
- expected_organism
- embargoed
- provenance_metadata
- external_database_identifiers
- gold_organism_identifiers
- collection_date
- samp_name
- host_taxid
- sample_isolation_method
- sample_isolated_from
- sample_collection_site
- sample_growth_conditions
- ploidy
- source_mat_id
slot_usage:
  id:
    name: id
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:osm-{id_shoulder}-{id_blade}$'
      interpolated: true
  expected_organism:
    name: expected_organism
    structured_pattern:
      syntax: '{id_nmdc_prefix}:orgn-{id_shoulder}-{id_blade}$'
      interpolated: true
  source_mat_id:
    name: source_mat_id
    description: Culture collection identifier for the source of this organism sample.
    comments:
    - On OrganismSample the slot identifies the catalog entry the strain was ordered
      from. CURIE form using a declared prefix is preferred (e.g. dsmz:DSM-15171,
      atcc:700808). Per-collection normalization rules and prefix-coverage gaps are
      documented in src/docs/jgi-isolate-field-routing.md.
    examples:
    - description: Ruegeria pomeroyi DSS-3 at DSMZ (bioregistry prefix dsmz; same
        strain as atcc:700808 and lmg:23168). Verified in GOLD organism_v2. https://www.dsmz.de/collection/catalogue/details/culture/DSM-15171
      object:
        type: nmdc:TextValue
        has_raw_value: dsmz:DSM-15171
    - description: Ruegeria pomeroyi DSS-3 at ATCC (bioregistry prefix atcc; same
        strain as dsmz:DSM-15171 and lmg:23168). Verified in GOLD organism_v2. https://www.atcc.org/products/700808
      object:
        type: nmdc:TextValue
        has_raw_value: atcc:700808
    - description: Ruegeria pomeroyi DSS-3 at BCCM/LMG (not yet in bioregistry; same
        strain as dsmz:DSM-15171 and atcc:700808). Verified in BCCM/LMG catalogue
        2026-04-30. https://bccm.belspo.be/catalogues/lmg-strain-details?NUM=23168
      object:
        type: nmdc:TextValue
        has_raw_value: lmg:23168
    - description: Pseudomonas putida KT2440 at JCM/RIKEN (bioregistry prefix jcm).
        http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=20004
      object:
        type: nmdc:TextValue
        has_raw_value: jcm:20004
    - description: Bacillus subtilis 168 at NBRC/NITE (bioregistry prefix nbrc). http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=13719
      object:
        type: nmdc:TextValue
        has_raw_value: nbrc:13719
    - description: Escherichia coli at BCRC/FIRDI (bioregistry prefix bcrc). https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=10694
      object:
        type: nmdc:TextValue
        has_raw_value: bcrc:10694
    see_also:
    - https://github.com/microbiomedata/nmdc-schema/issues/3036
    structured_aliases:
    - literal_form: Culture Collection and ID
      predicate: NARROW_SYNONYM
      contexts:
      - https://jgi.doe.gov/isolate-submission-form/v19
class_uri: nmdc:OrganismSample

name: OrganismSample
description: A material sample in which all cells are expected to share the same genome.
  This includes microbial colony picks, pellets from presumably pure liquid cultures,
  plant tissue clips, fungal fruiting body sections, and similar materials where the
  submitter intends to study a single organism. The purity expectation may be contradicted
  by sequencing results.
title: Organism Sample
comments:
- An OrganismSample is not necessarily pure. The submitter expects it to contain a
  single organism, but sequencing may reveal contamination. Purity and strain-verification
  fields (single-colony isolation, ribosomal sequences, fungal screening) are JGI
  submission logistics and live in submission-schema JgiIsolateInterface, not here.
- The expected_organism slot links to an Organism instance representing what the submitter
  believes is in the sample.
- The defining criterion is genomic homogeneity of intent, not material type. A bacterial
  colony pick, a plant leaf clip, and a fungal fruiting body section are all OrganismSamples
  because the submitter expects one genome. An algal mat, a cat fecal sample for microbiome
  study, or a soil sample are Biosamples because they contain communities of organisms.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://github.com/microbiomedata/nmdc-schema/issues/2803
- https://github.com/microbiomedata/nmdc-schema/issues/2961
close_mappings:
- OBI:0100051
is_a: Sample
slot_usage:
  id:
    name: id
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:osm-{id_shoulder}-{id_blade}$'
      interpolated: true
  expected_organism:
    name: expected_organism
    structured_pattern:
      syntax: '{id_nmdc_prefix}:orgn-{id_shoulder}-{id_blade}$'
      interpolated: true
  source_mat_id:
    name: source_mat_id
    description: Culture collection identifier for the source of this organism sample.
    comments:
    - On OrganismSample the slot identifies the catalog entry the strain was ordered
      from. CURIE form using a declared prefix is preferred (e.g. dsmz:DSM-15171,
      atcc:700808). Per-collection normalization rules and prefix-coverage gaps are
      documented in src/docs/jgi-isolate-field-routing.md.
    examples:
    - description: Ruegeria pomeroyi DSS-3 at DSMZ (bioregistry prefix dsmz; same
        strain as atcc:700808 and lmg:23168). Verified in GOLD organism_v2. https://www.dsmz.de/collection/catalogue/details/culture/DSM-15171
      object:
        type: nmdc:TextValue
        has_raw_value: dsmz:DSM-15171
    - description: Ruegeria pomeroyi DSS-3 at ATCC (bioregistry prefix atcc; same
        strain as dsmz:DSM-15171 and lmg:23168). Verified in GOLD organism_v2. https://www.atcc.org/products/700808
      object:
        type: nmdc:TextValue
        has_raw_value: atcc:700808
    - description: Ruegeria pomeroyi DSS-3 at BCCM/LMG (not yet in bioregistry; same
        strain as dsmz:DSM-15171 and atcc:700808). Verified in BCCM/LMG catalogue
        2026-04-30. https://bccm.belspo.be/catalogues/lmg-strain-details?NUM=23168
      object:
        type: nmdc:TextValue
        has_raw_value: lmg:23168
    - description: Pseudomonas putida KT2440 at JCM/RIKEN (bioregistry prefix jcm).
        http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=20004
      object:
        type: nmdc:TextValue
        has_raw_value: jcm:20004
    - description: Bacillus subtilis 168 at NBRC/NITE (bioregistry prefix nbrc). http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=13719
      object:
        type: nmdc:TextValue
        has_raw_value: nbrc:13719
    - description: Escherichia coli at BCRC/FIRDI (bioregistry prefix bcrc). https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=10694
      object:
        type: nmdc:TextValue
        has_raw_value: bcrc:10694
    see_also:
    - https://github.com/microbiomedata/nmdc-schema/issues/3036
    structured_aliases:
    - literal_form: Culture Collection and ID
      predicate: NARROW_SYNONYM
      contexts:
      - https://jgi.doe.gov/isolate-submission-form/v19
attributes:
  associated_studies:
    name: associated_studies
    description: The study associated with a resource.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: associated_studies
    owner: OrganismSample
    domain_of:
    - DataGeneration
    - Biosample
    - OrganismSample
    range: Study
    required: true
    multivalued: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'
      interpolated: true
  expected_organism:
    name: expected_organism
    description: The organism that the submitter expects to be present in this sample.
      May be contradicted by sequencing results.
    examples:
    - value: nmdc:orgn-99-abc123
      description: Reference to an Organism instance in organism_set
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: expected_organism
    owner: OrganismSample
    domain_of:
    - OrganismSample
    range: Organism
    structured_pattern:
      syntax: '{id_nmdc_prefix}:orgn-{id_shoulder}-{id_blade}$'
      interpolated: true
  embargoed:
    name: embargoed
    description: If true, the data are embargoed and not available for public access.
    todos:
    - make this required?
    - first apply to Biosample
    - try to apply to all Biosamples in a particular nmdc-server SubmissionMetadata?
    - applying to a Study may not be granular enough
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: embargoed
    owner: OrganismSample
    domain_of:
    - Biosample
    - OrganismSample
    range: boolean
    recommended: true
  provenance_metadata:
    name: provenance_metadata
    description: Provides information about the provenance of a record.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: provenance_metadata
    owner: OrganismSample
    domain_of:
    - Study
    - DataGeneration
    - Biosample
    - OrganismSample
    range: ProvenanceMetadata
  external_database_identifiers:
    name: external_database_identifiers
    description: Link to corresponding identifier in external database
    comments:
    - The value of this field is always a registered CURIE
    from_schema: https://w3id.org/nmdc/nmdc
    close_mappings:
    - skos:closeMatch
    rank: 1000
    is_a: alternative_identifiers
    abstract: true
    alias: external_database_identifiers
    owner: OrganismSample
    domain_of:
    - ProcessedSample
    - OrganismSample
    range: external_identifier
    multivalued: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
  gold_organism_identifiers:
    name: gold_organism_identifiers
    description: identifiers for corresponding organism in GOLD
    examples:
    - value: gold:Go0000058
      description: GOLD organism_v2 Campylobacter concisus 13826 (queried 2026-04-14)
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://github.com/microbiomedata/nmdc-schema/issues/2973
    rank: 1000
    is_a: external_database_identifiers
    mixins:
    - gold_identifiers
    alias: gold_organism_identifiers
    owner: OrganismSample
    domain_of:
    - OrganismSample
    range: uriorcurie
    multivalued: true
    pattern: ^gold:Go[0-9]+$
  collection_date:
    name: collection_date
    description: 'The time of sampling, either as an instance (single point in time)
      or interval. In case no exact time is available, the date/time can be right
      truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;
      2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'
    title: collection date
    examples:
    - value: '2013-03-25T12:42:31+01:00'
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    keywords:
    - date
    slot_uri: MIXS:0000011
    alias: collection_date
    owner: OrganismSample
    domain_of:
    - Biosample
    - OrganismSample
    range: TimestampValue
  samp_name:
    name: samp_name
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: ''
    description: A local identifier or name that for the material sample used for
      extracting nucleic acids, and subsequent sequencing. It can refer either to
      the original material collected or to any derived sub-samples. It can have any
      format, but we suggest that you make it concise, unique and consistent within
      your lab, and as informative as possible. INSDC requires every sample name from
      a single Submitter to be unique. Use of a globally unique identifier for the
      field source_mat_id is recommended in addition to sample_name
    title: sample name
    examples:
    - value: ISDsoil1
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    keywords:
    - sample
    slot_uri: MIXS:0001107
    alias: samp_name
    owner: OrganismSample
    domain_of:
    - Biosample
    - OrganismSample
    range: string
  host_taxid:
    name: host_taxid
    annotations:
      Expected_value:
        tag: Expected_value
        value: NCBI taxon identifier
    description: NCBI taxon id of the host, e.g. 9606
    title: host taxid
    comments:
    - Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value
    from_schema: https://w3id.org/nmdc/nmdc
    structured_aliases:
    - literal_form: Host NCBI Taxonomy ID
      predicate: EXACT_SYNONYM
      contexts:
      - https://jgi.doe.gov/isolate-submission-form/v19
    rank: 1000
    keywords:
    - host
    - host.
    - taxon
    slot_uri: MIXS:0000250
    alias: host_taxid
    owner: OrganismSample
    domain_of:
    - Biosample
    - OrganismSample
    range: ControlledIdentifiedTermValue
  sample_isolation_method:
    name: sample_isolation_method
    description: Method, protocol, or kit used to extract DNA/RNA from the sample.
    comments:
    - See also dna_isolate_meth in submission-schema for the equivalent portal field.
    examples:
    - value: Wizard Genomic DNA Purification Kit
      description: Promega Wizard kit — a widely-used DNA isolation method in JGI
        bacterial isolate submissions
    in_subset:
    - jgi_isolate
    from_schema: https://w3id.org/nmdc/nmdc
    structured_aliases:
    - literal_form: Sample Isolation Method
      predicate: EXACT_SYNONYM
      contexts:
      - https://jgi.doe.gov/isolate-submission-form/v19
    rank: 1000
    alias: sample_isolation_method
    owner: OrganismSample
    domain_of:
    - OrganismSample
    range: string
  sample_isolated_from:
    name: sample_isolated_from
    description: Free-text description of the environmental or biological matrix from
      which the organism sample was isolated — the *what* it came out of (e.g. iron-rich
      microbial mat, leaf tissue, catalog vial). For the *where* (geographic / environmental
      site of collection) see `sample_collection_site`; for in-vitro growth conditions
      (lab maintenance, culture media, growth chambers) see `sample_growth_conditions`.
    todos:
    - 'Redesign in #3054 will sharpen the boundary between this slot and the sample_collection_site
      / sample_growth_conditions siblings.'
    comments:
    - Routes JGI Isolate (NA) v19 form field 44 ("Sample Isolated From"). Field 45
      ("Collection Site or Growth Conditions") routes to `sample_collection_site`
      or `sample_growth_conditions` depending on which half the submitter is reporting.
    - 'Used when no upstream Biosample carries env-triad information (e.g. culture
      collection orders, lab-derived samples). When a linked Biosample is available,
      environmental provenance belongs there. Not a typed reference — future work
      may add a structured slot or wrapper class for typed sample-to-sample links;
      see #3033 and #3054.'
    examples:
    - value: Iron-rich microbial mat from hydrothermal vent, Naha Vents, south rift
        of Loihi seamount, Hawaii
      description: GOLD organism_v2 Go0000189 (Shewanella loihica PV-4, queried 2026-04-21)
    - value: Saltwater from water column off the Georgia coast, USA
      description: GOLD organism_v2 Go0000514 (Ruegeria pomeroyi DSS-3, queried 2026-04-21)
    - value: DSMZ catalog vial (DSM 6125)
      description: Catalog-collection origin — no environmental matrix upstream
    in_subset:
    - jgi_isolate
    from_schema: https://w3id.org/nmdc/nmdc
    structured_aliases:
    - literal_form: Sample Isolated From
      predicate: EXACT_SYNONYM
      contexts:
      - https://jgi.doe.gov/isolate-submission-form/v19
    rank: 1000
    alias: sample_isolated_from
    owner: OrganismSample
    domain_of:
    - OrganismSample
    range: string
  sample_collection_site:
    name: sample_collection_site
    description: Free-text description of the place where the sample was collected
      — the geographic / environmental site or named location.
    comments:
    - On `OrganismSample`, this slot routes the collection-site half of JGI Isolate
      (NA) v19 form field 45 ("Collection Site or Growth Conditions"). The growth-conditions
      half routes to `sample_growth_conditions`. The submitter populates one or the
      other depending on whether the sample came from a field collection or from in-vitro
      maintenance.
    from_schema: https://w3id.org/nmdc/nmdc
    structured_aliases:
    - literal_form: Collection Site or Growth Conditions
      predicate: NARROW_SYNONYM
      contexts:
      - https://jgi.doe.gov/isolate-submission-form/v19
    rank: 1000
    alias: sample_collection_site
    owner: OrganismSample
    domain_of:
    - Biosample
    - OrganismSample
    range: string
  sample_growth_conditions:
    name: sample_growth_conditions
    description: Free-text description of the in-vitro conditions under which the
      organism sample was grown or maintained — culture media, growth chamber settings,
      facility type, or other lab-controlled growth context. For environmental site
      context see `sample_collection_site`; for the source matrix the organism came
      out of see `sample_isolated_from`.
    comments:
    - On `OrganismSample`, this slot routes the growth-conditions half of JGI Isolate
      (NA) v19 form field 45 ("Collection Site or Growth Conditions"). The collection-site
      half routes to `sample_collection_site`. The submitter populates one or the
      other depending on whether the sample came from a field collection or from in-vitro
      maintenance.
    - Distinct from MIxS `isol_growth_condt` (MIXS:0000003), which expects a publication
      reference (DOI/PMID/URL pattern), not free-text growth conditions.
    examples:
    - value: Greenhouse-grown
      description: Plant-tissue isolate maintained in greenhouse conditions
    - value: Cultivated indoor; substrate logs of supplemented oak
      description: Mushroom (Lentinula edodes) cultivation context
    - value: E. coli K-12 MG1655 broth culture infected with phage T4
      description: Viral-isolate growth context — host culture conditions
    in_subset:
    - jgi_isolate
    from_schema: https://w3id.org/nmdc/nmdc
    structured_aliases:
    - literal_form: Collection Site or Growth Conditions
      predicate: NARROW_SYNONYM
      contexts:
      - https://jgi.doe.gov/isolate-submission-form/v19
    rank: 1000
    alias: sample_growth_conditions
    owner: OrganismSample
    domain_of:
    - OrganismSample
    range: string
  ploidy:
    name: ploidy
    description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid,
      triploid, tetraploid). It has implications for the downstream study of duplicated
      gene and regions of the genomes (and perhaps for difficulties in assembly).
      For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic
      Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer
      to http://purl.bioontology.org/ontology/PATO
    title: ploidy
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: MIXS:0000021
    alias: ploidy
    owner: OrganismSample
    domain_of:
    - OrganismSample
    range: PloidyEnum
  source_mat_id:
    name: source_mat_id
    annotations:
      Expected_value:
        tag: Expected_value
        value: 'for cultures of microorganisms: identifiers for two culture collections;
          for other material a unique arbitrary identifer'
    description: Culture collection identifier for the source of this organism sample.
    title: source material identifiers
    comments:
    - On OrganismSample the slot identifies the catalog entry the strain was ordered
      from. CURIE form using a declared prefix is preferred (e.g. dsmz:DSM-15171,
      atcc:700808). Per-collection normalization rules and prefix-coverage gaps are
      documented in src/docs/jgi-isolate-field-routing.md.
    examples:
    - description: Ruegeria pomeroyi DSS-3 at DSMZ (bioregistry prefix dsmz; same
        strain as atcc:700808 and lmg:23168). Verified in GOLD organism_v2. https://www.dsmz.de/collection/catalogue/details/culture/DSM-15171
      object:
        type: nmdc:TextValue
        has_raw_value: dsmz:DSM-15171
    - description: Ruegeria pomeroyi DSS-3 at ATCC (bioregistry prefix atcc; same
        strain as dsmz:DSM-15171 and lmg:23168). Verified in GOLD organism_v2. https://www.atcc.org/products/700808
      object:
        type: nmdc:TextValue
        has_raw_value: atcc:700808
    - description: Ruegeria pomeroyi DSS-3 at BCCM/LMG (not yet in bioregistry; same
        strain as dsmz:DSM-15171 and atcc:700808). Verified in BCCM/LMG catalogue
        2026-04-30. https://bccm.belspo.be/catalogues/lmg-strain-details?NUM=23168
      object:
        type: nmdc:TextValue
        has_raw_value: lmg:23168
    - description: Pseudomonas putida KT2440 at JCM/RIKEN (bioregistry prefix jcm).
        http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=20004
      object:
        type: nmdc:TextValue
        has_raw_value: jcm:20004
    - description: Bacillus subtilis 168 at NBRC/NITE (bioregistry prefix nbrc). http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=13719
      object:
        type: nmdc:TextValue
        has_raw_value: nbrc:13719
    - description: Escherichia coli at BCRC/FIRDI (bioregistry prefix bcrc). https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=10694
      object:
        type: nmdc:TextValue
        has_raw_value: bcrc:10694
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://github.com/microbiomedata/nmdc-schema/issues/3036
    structured_aliases:
    - literal_form: Culture Collection and ID
      predicate: NARROW_SYNONYM
      contexts:
      - https://jgi.doe.gov/isolate-submission-form/v19
    rank: 1000
    keywords:
    - identifier
    - material
    - source
    slot_uri: MIXS:0000026
    alias: source_mat_id
    owner: OrganismSample
    domain_of:
    - Biosample
    - OrganismSample
    range: TextValue
    multivalued: false
  id:
    name: id
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI
    notes:
    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'
    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters
      will be accepted
    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked
      via per-class id slot usage assertions
    - minting authority shoulders should probably be enumerated and checked in the
      pattern
    examples:
    - value: nmdc:mgmag-00-x012.1_7_c1
      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248
    from_schema: https://w3id.org/nmdc/nmdc
    structured_aliases:
    - literal_form: workflow_execution_id
      predicate: NARROW_SYNONYM
      contexts:
      - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
    - literal_form: data_object_id
      predicate: NARROW_SYNONYM
      contexts:
      - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
    rank: 1000
    identifier: true
    alias: id
    owner: OrganismSample
    domain_of:
    - NamedThing
    range: uriorcurie
    required: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
    structured_pattern:
      syntax: '{id_nmdc_prefix}:osm-{id_shoulder}-{id_blade}$'
      interpolated: true
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: name
    owner: OrganismSample
    domain_of:
    - PersonValue
    - NamedThing
    - Protocol
    range: string
  description:
    name: description
    description: a human-readable description of a thing
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: dcterms:description
    alias: description
    owner: OrganismSample
    domain_of:
    - ImageValue
    - NamedThing
    - Protocol
    range: string
  alternative_identifiers:
    name: alternative_identifiers
    description: A list of alternative identifiers for the entity.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: alternative_identifiers
    owner: OrganismSample
    domain_of:
    - NamedThing
    - MetaboliteIdentification
    range: uriorcurie
    multivalued: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,\(\)\=\#]*$
  type:
    name: type
    description: the class_uri of the class that has been instantiated
    notes:
    - makes it easier to read example data files
    - required for polymorphic MongoDB collections
    examples:
    - value: nmdc:Biosample
    - value: nmdc:Study
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://github.com/microbiomedata/nmdc-schema/issues/1048
    - https://github.com/microbiomedata/nmdc-schema/issues/1233
    - https://github.com/microbiomedata/nmdc-schema/issues/248
    structured_aliases:
    - literal_form: workflow_execution_class
      predicate: NARROW_SYNONYM
      contexts:
      - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    alias: type
    owner: OrganismSample
    domain_of:
    - EukEval
    - FunctionalAnnotationAggMember
    - PeptideQuantification
    - ProteinQuantification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - OntologyRelation
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    - ProvenanceMetadata
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    range: uriorcurie
    required: true
class_uri: nmdc:OrganismSample